The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes
Open accessAbstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Interestingly, inactivating mutations and/or reduced expression of JmjC histone demethylases including JARID1C (Dalgliesh et al, 2010), UTX (van Haaften et al, 2009) and JHDM1B/FBXL10 (Frescas et al, 2007), occur in RCCs, multiple myeloma, glioblastoma multiforme and several other cancers.”
From The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases (2011) · cites this paper as Dalgliesh et al, 2010
In the citing paper
“A number of 2-oxoglutarate-dependent enzymes that act on chromatin are themselves targets of inactivating mutations in cancer, including the UTX H3K27 demethylase (also called KDM6A), JARID1C H3K4 demethylase (KDM5C), and TET2, making them attractive candidates for pathogenically relevant inhibition by succinate, fumarate, and R-2HG (Abdel-Wahab et al., 2009; Dalgliesh et al., 2010; Tefferi et al”
From Influence of Metabolism on Epigenetics and Disease (2013) · cites this paper as Dalgliesh et al., 2010
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
(2016) · Springer eBooks · doi:10.1007/978-3-319-40618-3 · Cited by 17,300
An Integrated Genomic Analysis of Human Glioblastoma Multiforme
Parsons, D. W., Jones, S., Zhang, X., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.-M., Gallia, G. L., et al. (2008) · Science · doi:10.1126/science.1164382 · Cited by 5,857
Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
Jones, S., Zhang, X., Parsons, D. W., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Kamiyama, H., Jimeno, A., et al. (2008) · Science · doi:10.1126/science.1164368 · Cited by 3,969
Self-citationPatterns of somatic mutation in human cancer genomes
Greenman, C. D., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., Bignell, G. R., Davies, H. R., Teague, J. W., Butler, A. P., Stevens, C., et al. (2007) · Nature · doi:10.1038/nature05610 · Cited by 3,143
Self-citationPrognostic significance of morphologic parameters in renal cell carcinoma
Fuhrman, S. A., Lasky, L. C., & Limas, C. (1982) · The American Journal of Surgical Pathology · doi:10.1097/00000478-198210000-00007 · Cited by 2,744
Rini, B. I., Campbell, S. C., & Escudier, B. J. (2009) · The Lancet · doi:10.1016/s0140-6736(09)60229-4 · Cited by 1,634
Pathology and genetics of tumours of the urinary system and male genital organs
Eble, J. N. (2004) · Cited by 1,015
Zhang, H., Gao, P., Fukuda, R., Kumar, G., Krishnamachary, B., Zeller, K. I., Dang, C. V., & Semenza, G. L. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.04.001 · Cited by 885
Demethylation of H3K27 Regulates Polycomb Recruitment and H2A Ubiquitination
Lee, M. G., Villa, R., Trojer, P., Norman, J. A., Yan, K.-P., Reinberg, D., Croce, L. D., & Shiekhattar, R. (2007) · Science · doi:10.1126/science.1149042 · Cited by 789
Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer
van Haaften, G., Dalgliesh, G. L., Davies, H., Chen, L., Bignell, G., Greenman, C., Edkins, S., Hardy, C., O'Meara, S., Teague, J., et al. (2009) · Nature Genetics · doi:10.1038/ng.349 · Cited by 784
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 201–300 of 1,000
Editing the Epigenome: Reshaping the Genomic Landscape
Holtzman, L., & Gersbach, C. A. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021632 · Cited by 147
“When studying primary samples from human patients, it is often challenging to distinguish between correlation and causality of the epigenetic component, but multiple studies have revealed aberrant patterns of epigenetic components in many types of cancer that correlate with its progression and outcome (4, 5, 14, 36, 9…”
BackgroundClear Cell Renal Cell Carcinoma Subtypes Identified by BAP1 and PBRM1 Expression
Joseph, R. W., Kapur, P., Serie, D., Parasramka, M. A., Ho, T. H., Cheville, J. C., Frenkel, E. P., Parker, A. S., & Brugarolas, J. (2015) · The Journal of Urology · doi:10.1016/j.juro.2015.07.113 · Cited by 143
X-chromosome inactivation and escape
Distèche, C. M., & Berletch, J. B. (2015) · Journal of Genetics · doi:10.1007/s12041-015-0574-1 · Cited by 146
Malouf, G. G., Su, X., Yao, H., Gao, J., Xiong, L., He, Q., Compérat, É., Couturier, J., Molinié, V., Escudier, B. J., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-3036 · Cited by 138
“The second case (RCCT2) had a missense mutation of KDM5C gene, which acts as a histone H3 lysine 4 demethylase and is frequently inactivated in ccRCC (17).”
BackgroundSelf-citationToledo, R. A., Qin, Y., Cheng, Z.-M., Gao, Q., Iwata, S., Silva, G. M., Prasad, M. L., Ocal, I. T., Rao, S. N., D, N. A. M., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1841 · Cited by 146
“SETD2 is a K36 methyltransferase frequently mutated in renal cancers and leukemias (27, 28), suggesting that this variant is pathogenically relevant.”
BackgroundEpigenetic regulation of signaling pathways in cancer: Role of the histone methyltransferase EZH2
Tsang, D. P., & Cheng, A. S. L. (2010) · Journal of Gastroenterology and Hepatology · doi:10.1111/j.1440-1746.2010.06447.x · Cited by 141
Outchkourov, N. S., Muiño, J. M., Kaufmann, K., van IJcken, W. F. J., Koerkamp, M. J. A. G., van Leenen, D., de Graaf, P., Holstege, F. C. P., Grosveld, F. G., & Timmers, H. T. M. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.02.030 · Cited by 139
“SMCX or JARID1C) has been implicated in different human diseases, such as renal cancer and X-linkedmental retardation (Blair et al., 2011; Dalgliesh et al., 2010).”
BackgroundInfluentialA Comprehensive Review of Lysine-Specific Demethylase 1 and its Roles in Cancer
Hosseini, A., & Minucci, S. (2017) · Epigenomics · doi:10.2217/epi-2017-0022 · Cited by 139
Gossage, L., Murtaza, M., Slatter, A. F., Lichtenstein, C. P., Warren, A. Y., Haynes, B., Marass, F., Roberts, I., Shanahan, S. J., Claas, A., et al. (2013) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22116 · Cited by 137
Mutations of epigenetic regulatory genes are common in thymic carcinomas
Wang, Y., Thomas, A., Lau, C. C., Rajan, A., Zhu, Y. J., Killian, J. K., Petrini, I., Pham, T. C., Morrow, B., Zhong, X., et al. (2014) · Scientific Reports · doi:10.1038/srep07336 · Cited by 135
Arai, E., Chiku, S., Mori, T., Gotoh, M., Nakagawa, T., Fujimoto, H., & Kanai, Y. (2012) · Carcinogenesis · doi:10.1093/carcin/bgs177 · Cited by 134
“Such efforts have revealed that renal carcinogenesis involves inactivation of histone-modifying genes, such as SETD2 (7), a histone H3 lysine 36 methyltransferase, JARIDIC (KDM5C (7)), a histone H3 lysine 4 demethylase, and UTX (KMD6A (8)), a histone H3 lysine 27 demethylase, as well as the SWI/SNF chromatin-remodelin…”
BackgroundKMT2D maintains neoplastic cell proliferation and global histone H3 lysine 4 monomethylation
Guo, C., Chen, L. H., Huang, Y., Chang, C., Wang, P., Pirozzi, C. J., Qin, X., Bao, X., Greer, P. K., McLendon, R. E., et al. (2013) · Oncotarget · doi:10.18632/oncotarget.1555 · Cited by 136
“Additional cancers that have recently been found to be driven by an aberrant KMT2D/KMT2C pathway, with frequencies ranging from 5% to 40%, include renal [2], prostate [18], bladder [5], gastric [11], hepatic [3] and lung cancer [6, 19].”
Self-citationMalouf, G. G., Ali, S. M., Wang, K., Balasubramanian, S., Ross, J. S., Miller, V. A., Stephens, P. J., Khayat, D., Pal, S. K., Su, X., et al. (2016) · European Urology · doi:10.1016/j.eururo.2016.01.051 · Cited by 133
Self-citationHorton, J. R., Engstrom, A., Zoeller, E. L., Liu, X., Shanks, J. R., Zhang, X., Johns, M. A., Vertino, P. M., Fu, H., & Cheng, X. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.698449 · Cited by 132
“KDM5C, on the other hand, exhibits loss-of-function alterations in 7% of clear cell renal cell carcinomas (73), where it plays a tumor-suppressive role (74), and inherited mutations in KDM5C are associated with X-linked mental retardation.”
BackgroundShaping the cellular landscape with Set2/SETD2 methylation
McDaniel, S. L., & Strahl, B. D. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2517-x · Cited by 130
Merlin: a tumour suppressor with functions at the cell cortex and in the nucleus
Li, W., Cooper, J. M., Karajannis, M. A., & Giancotti, F. G. (2012) · EMBO Reports · doi:10.1038/embor.2012.11 · Cited by 130
PBRM1 and BAP1 as Novel Targets for Renal Cell Carcinoma
Brugarolas, J. (2013) · The Cancer Journal · doi:10.1097/ppo.0b013e3182a102d1 · Cited by 133
Ochocki, J. D., Khare, S., Hess, M., Ackerman, D., Qiu, B., Daisak, J. I., Worth, A. J., Lin, N., Lee, P., Xie, H. J., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.04.009 · Cited by 128
“Recent large-scale analyses identified frequent mutations in three genes, PBRM1 ( 40%), SETD2 ( 15%), and BAP1 ( 15%), all of which encode epigenetic regulators and reside in a 43 Mb region on chromosome 3p that encompasses VHL (Dalgliesh et al., 2010; Peña-Llopis et al., 2012; Sato et al., 2013; Cancer Genome Atlas…”
InfluentialMutation of cancer driver MLL2 results in transcription stress and genome instabilityPreprint
Kantidakis, T., Saponaro, M., Mitter, R., Horswell, S. D., Kranz, A., Boeing, S., Aygün, O., Kelly, G. P., Matthews, N., Stewart, A., et al. (2016) · Genes & Development · doi:10.1101/gad.275453.115 · Cited by 130
“…(Kasaian et al. 2013), esophageal squamous cell carcinoma (Gao et al. 2014; Song et al. 2014), head and neck squamous carcinomas (Seiwert et al. 2015), renal carcinoma (Dalgliesh et al. 2010), urothelial bladder carcinoma (Balbas-Martinez et al. 2013), and prostate cancer (Grasso et al. 2012).”
BackgroundTao, Y., Ruan, J., Yeh, S., Lu, X., Wang, Y., Zhai, W., Cai, J., Ling, S., Gong, Q., Chong, Z., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108715108 · Cited by 131
“As a result, the frequency spectrum of mutations in a local cell population is expected to be strongly bimodal, with mutations at either very high or very low frequencies (6, 7).”
BackgroundThe epigenetic landscape of renal cancer
Morris, M. R., & Latif, F. (2016) · Nature Reviews Nephrology · doi:10.1038/nrneph.2016.168 · Cited by 129
A clear picture of renal cell carcinoma
Hakimi, A. A., Pham, C. G., & Hsieh, J. J.-D. (2013) · Nature Genetics · doi:10.1038/ng.2708 · Cited by 135
Kovac, M. B., Navas, C., Horswell, S. D., Salm, M., Bardella, C., Rowan, A., Stares, M., Castro-Giner, F., Fisher, R. A., de Bruin, E. C., et al. (2015) · Nature Communications · doi:10.1038/ncomms7336 · Cited by 123
Peña‐Llopis, S., & Brugarolas, J. (2013) · Nature Protocols · doi:10.1038/nprot.2013.141 · Cited by 122
Chromatin as an oxygen sensor and active player in the hypoxia response
Melvin, A., & Rocha, S. (2011) · Cellular Signalling · doi:10.1016/j.cellsig.2011.08.019 · Cited by 123
Sankin, A. I., Hakimi, A. A., Mikkilineni, N., Ostrovnaya, I., Silk, M. T., Liang, Y., Mano, R., Chevinsky, M. S., Motzer, R. J., Solomon, S. B., et al. (2014) · Cancer Medicine · doi:10.1002/cam4.293 · Cited by 127
“These studies confirmed recurrent mutations in the chromatin-modulating genes polybromo 1 (PBRM1) [16], SET domain containing 2 (SETD2) [17, 18], BRCA1-associated protein-1 (BAP1) [19], and lysine (K)-specific demethylase 5C (KDM5C) [17] in kidney cancer.”
BackgroundWhite, S. M., Avantaggiati, M. L., Nemazanyy, I., Poto, C. D., Yang, Y., Pende, M., Gibney, G. T., Ressom, H. W., Field, J., Atkins, M. B., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.04.014 · Cited by 121
The Impact of External Factors on the Epigenome:In Uteroand over Lifetime
Toraño, E. G., García, M. G., Fernández-Morera, J. L., García, P. N., & Fernández, A. F. (2016) · BioMed Research International · doi:10.1155/2016/2568635 · Cited by 130
“Alterations in histonemodifying enzymes have been identified as the main cause of these changes in many cases [63–66] and as a result they have started to gain importance as a therapeutic target in recent years [67–69].”
BackgroundGenomic Medicine Frontier in Human Solid Tumors: Prospects and Challenges
Dienstmann, R., Rodon, J. A., Barretina, J., & Tabernero, J. M. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.45.2268 · Cited by 120
Goode, B., Joseph, N. M., Stevers, M., Ziffle, J. V., Onodera, C. S., Talevich, E., Grenert, J. P., Yeh, I., Bastian, B. C., Phillips, J. J., et al. (2017) · Modern Pathology · doi:10.1038/modpathol.2017.153 · Cited by 118
“21,22 Two tumors contained missense mutations in LRP1B, which encodes a lipoprotein receptor-related protein.”
Current and future systemic treatments for renal cell carcinoma
Fisher, R. A., Gore, M. E., & Larkin, J. (2012) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2012.06.004 · Cited by 117
Chiba, T., Saito, T., Yuki, K., Zen, Y., Koide, S., Kanogawa, N., Motoyama, T., Ogasawara, S., Suzuki, E., Ooka, Y., et al. (2014) · International Journal of Cancer · doi:10.1002/ijc.28985 · Cited by 119
Brannon, A. R., Haake, S. M., Hacker, K. E., Pruthi, R. S., Wallen, E., Nielsen, M. E., & Rathmell, W. K. (2011) · European Urology · doi:10.1016/j.eururo.2011.10.007 · Cited by 116
“[9] were processed on different chip series at different”
BackgroundMethodMedical treatment of renal cancer: new horizons
Greef, B., & Eisen, T. G. (2016) · British Journal of Cancer · doi:10.1038/bjc.2016.230 · Cited by 114
“…Varela et al, 2011; Hakimi et al, 2013; Gossage et al, 2014), BRCA1-associated protein 1 (BAP1; 6– 15%; Peña-Llopis et al, 2012; Hakimi et al, 2013; Gossage et al, 2014) and SET domain containing 2 (SETD2; 3–16%; Dalgliesh et al, 2010; Duns et al, 2010; Hakimi et al, 2013; Gossage et al, 2014).”
BackgroundLncRNAs Expression Signatures of Renal Clear Cell Carcinoma Revealed by Microarray
Gan, Y., Yao, W., Wang, J., Ma, X., Xiao, W., Li, H., Xia, D., Yang, Y., Deng, K., Xiao, H., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042377 · Cited by 115
Sex Chromosome Effects on Male–Female Differences in Mammals
Snell, D. M., & Turner, J. M. A. (2018) · Current Biology · doi:10.1016/j.cub.2018.09.018 · Cited by 114
Koçak, B., Durmaz, E. Ş., Kuş, E. A., & Ulusan, M. B. (2019) · American Journal of Roentgenology · doi:10.2214/ajr.18.20443 · Cited by 120
Human genetics and genomics a decade after the release of the draft sequence of the human genome
Naidoo, N., Yudi Pawitan, Y., Soong, R., Cooper, D. N., & Ku, C. (2011) · Human Genomics · doi:10.1186/1479-7364-5-6-577 · Cited by 117
Choi, H., Park, J., Park, M., Won, H., Joo, H.-S., Lee, C. H., Lee, J., & Kong, G. (2015) · EMBO Reports · doi:10.15252/embr.201540244 · Cited by 113
“Furthermore, genomewide analyses have identified various somatic mutations and deletions of UTX in several human cancers, including breast, bladder, and renal cancers and leukaemia [12 – 14].”
Rydzanicz, M., Wrzesiński, T., Bluyssen, H. A. R., & Wesoły, J. (2013) · Cancer Letters · doi:10.1016/j.canlet.2013.08.006 · Cited by 112
Yu, Z., Lv, Y., Su, C., Lu, W., Zhang, R., Li, J., Guo, B., Yan, H., Liu, D., Yang, Z., et al. (2023) · Cancer Research · doi:10.1158/0008-5472.can-22-2224 · Cited by 116
Enhancer deregulation in cancer and other diseases
Herz, H. (2016) · BioEssays · doi:10.1002/bies.201600106 · Cited by 110
Methylation biomarkers for early cancer detection and diagnosis: Current and future perspectives
Ibrahim, J., Peeters, M., Camp, G. V., & de Beeck, K. O. (2022) · European Journal of Cancer · doi:10.1016/j.ejca.2022.10.015 · Cited by 116
H3K36me3, message from chromatin to DNA damage repair
Sun, Z., Zhang, Y., Jia, J., Fang, Y., Tang, Y., Wu, H., & Fang, D. (2020) · Cell & Bioscience · doi:10.1186/s13578-020-0374-z · Cited by 109
Interplay Between pVHL and mTORC1 Pathways in Clear-Cell Renal Cell Carcinoma
Kucejová, B., Peña‐Llopis, S., Yamasaki, T., Sivanand, S., Tran, T. A. T., Alexander, S., Wolff, N. C., Lotan, Y., Xie, X.-J., Kabbani, W., et al. (2011) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-11-0302 · Cited by 118
“Although targeted sequencing studies have failed to identify activating mutations in Rheb and RhebL1 (2), recently, mutations in the mTOR gene itself were identified in ccRCC (32, 46).”
BackgroundMethodSankaran, S. M., Wilkinson, A. W., Elias, J. E., & Gozani, O. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.720748 · Cited by 109
Wrzesiński, T., Szeląg, M., Cieślikowski, W. A., Ida, A., Giles, R. H., Zodro, E., Szumska, J., Poźniak, J., Kwias, Z., Bluyssen, H. A. R., et al. (2015) · BMC Cancer · doi:10.1186/s12885-015-1530-4 · Cited by 103
“In case of ccRCC, up-or down-regulation of different TMEMs is supported by a number of microarray experiments [13 – 19].”
Histone-Modifying Enzymes: Regulators of Developmental Decisions and Drivers of Human Disease
Napierala, J. S., Koutelou, E., Schibler, A. C., & Dent, S. (2012) · Epigenomics · doi:10.2217/epi.12.3 · Cited by 111
The Kdm5 Family of Histone Demethylases as Targets in Oncology Drug Discovery
Rasmussen, P. B., & Staller, P. (2014) · Epigenomics · doi:10.2217/epi.14.14 · Cited by 108
Gu, B., & Lee, M. (2013) · Cell & Bioscience · doi:10.1186/2045-3701-3-39 · Cited by 113
“SMCX is an X-chromosome gene that escapes from X inactivation [149] and is often mutated in renal tumors and X-linked mental retardation (XLMR), suggesting that it has important functions in the human kidneys and brain [150,151].”
BackgroundNakada, C., Tsukamoto, Y., Matsuura, K., Nguyen, T. L., Hijiya, N., Uchida, T., Sato, F., Mimata, H., Seto, M., & Moriyama, M. (2011) · The Journal of Pathology · doi:10.1002/path.2860 · Cited by 108
New Strategies in Renal Cell Carcinoma: Targeting the Genetic and Metabolic Basis of Disease
Srinivasan, R., Ricketts, C. J., Sourbier, C., & Linehan, W. M. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-2993 · Cited by 111
“The Cancer Genome Atlas (TCGA) performed a comprehensive molecular characterization of more than 400 ccRCCs and identified 19 significantly mutated genes, including VHL and other chromosome 3 genes such as PBRM1, SETD2, and BAP1, as well as KDM5C, PTEN, MTOR,TP53, andPIK3CA.”
BackgroundInfluentialThe histone demethylase UTX/KDM6A in cancer: Progress and puzzles
Schulz, W. A., Lang, A., Koch, J., & Greife, A. (2019) · International Journal of Cancer · doi:10.1002/ijc.32116 · Cited by 105
Davidson, G., Helleux, A., Vano, Y. A., Lindner, V., Fattori, A., Cerciat, M., Elaidi, R., Verkarre, V., Sun, C., Chevreau, C., et al. (2023) · Cancer Research · doi:10.1158/0008-5472.can-22-3034 · Cited by 113
Selection of metastasis competent subclones in the tumour interior
Zhao, Y., Fu, X., Lopez, J. I., Rowan, A., Au, L., Fendler, A., Hazell, S., Xu, H., Horswell, S., Shepherd, S. T. C., et al. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01456-6 · Cited by 95
New Developments in the Pathogenesis and Therapeutic Targeting of the IDH1 Mutation in Glioma
Dimitrov, L., Hong, C. S., Yang, C., Zhuang, Z., & Heiss, J. D. (2015) · International Journal of Medical Sciences · doi:10.7150/ijms.11047 · Cited by 108
“Perhaps, the most significant study demonstrating that the tumorigenic effects of the IDH1 mutation arise due to TET2 dysfunction was the discovery that IDH1/2 and TET2 mutations were mutually exclusive in 300 AML samples [69].”
BackgroundInfluentialNucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes
Chen, X., Chen, Z., Chen, H., Su, Z., Yang, J., Lin, F., Shi, S., & He, X. (2012) · Science · doi:10.1126/science.1217580 · Cited by 103
The diverse roles of SPOP in prostate cancer and kidney cancer
Wang, Z. P., Song, Y., Ye, M., Dai, X., Zhu, X., & Wei, W. (2020) · Nature Reviews Urology · doi:10.1038/s41585-020-0314-z · Cited by 104
Schütte, U., Bisht, S., Heukamp, L. C., Kebschull, M., Florin, A., Haarmann, J., Hoffmann, P., Bendas, G., Buettner, R., Brossart, P., et al. (2014) · Translational Oncology · doi:10.1016/j.tranon.2014.02.005 · Cited by 106
Grafodatskaya, D., Chung, B. H., Butcher, D. T., Turinsky, A. L., Goodman, S. J., Choufani, S., Chen, Y. A., Lou, Y., Zhao, C., Rajendram, R., et al. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-1 · Cited by 103
“Due to common nature of diabetes we have included samples with this disease into our control dataset, but have excluded ovarian cancer samples because cancer as well as cancer therapies are known to alter epigenetic marks [51] and somatic KDM5C mutation was previously identified in cancer [52,53]; trisomy 21 cases wer…”
BackgroundShinagare, A. B., Vikram, R., Jaffe, C. C., Akın, O., Kirby, J., Huang, E. P., Freymann, J., Sainani, N. I., Sadow, C. A., Bathala, T. K., et al. (2015) · Abdominal Imaging · doi:10.1007/s00261-015-0386-z · Cited by 104
Global identification of MLL2-targeted loci reveals MLL2’s role in diverse signaling pathways
Guo, C., Chang, C.-C., Wortham, M., Chen, L. H., Kernagis, D., Qin, X., Cho, Y., Chi, J., Grant, G. A., McLendon, R. E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208807109 · Cited by 101
Self-citationLiu, W., Lindberg, J., Sui, G., Luo, J., Egevad, L., Li, T., Xie, C., Wan, M., Kim, S.-T., Wang, Z., et al. (2011) · Oncogene · doi:10.1038/onc.2011.554 · Cited by 100
“Multiple chromatinremodeling genes have recently been implicated through mutational analyses of various cancer types, such as renal cell (Dalgliesh et al., 2010), ovarian (Jones et al., 2010), lung (Medina et al., 2008) and others (Weissman and Knudsen, 2009), emphasizing the importance of this…”
Yabe, M., Miranda, R. N., & Medeiros, L. J. (2018) · Human Pathology · doi:10.1016/j.humpath.2018.01.005 · Cited by 101
JMJD family proteins in cancer and inflammation
Wang, M., Jianxin, X., Hong, W., Chen, S., & Huashan, S. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01145-1 · Cited by 106
“UTX is highly mutated across various cancers, including acute lymphoblastic leukemia,(303) chronic myelomonocytic leukemia,(304) bladder cancer,(305) medulloblastoma,(306) prostate cancer,(307) and renal carcinoma.(308) The proliferation of cancer cells was reduced when inactivating UTX mutations were resumed with the…”
BackgroundWartman, L. D., Larson, D. E., Xiang, Z., Ding, L., Chen, K., Lin, L., Cahan, P., Klco, J. M., Welch, J. S., Li, C., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci45284 · Cited by 101
Cooperation and Antagonism among Cancer Genes: The Renal Cancer Paradigm
Peña‐Llopis, S., Christie, A. L., Xie, X.-J., & Brugarolas, J. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-0360 · Cited by 101
“Adding to the challenge of uncovering genetic interactions (as determined by the frequency of VHL mutations detected), mutation sensitivity was seemingly low across all of the studies available (16, 17, 29).”
Genomic Heterogeneity of Translocation Renal Cell Carcinoma
Malouf, G. G., Monzon, F. A., Couturier, J., Molinié, V., Escudier, B. J., Camparo, P., Su, X., Yao, H., Tamboli, P., Lopez-Terrada, D. H., et al. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3825 · Cited by 99
“However, other tumor suppressor genes with roles in RCC biology have been recently identified in 3p (PBRM1, SETD2 and BAP1), and thus 3p loss in tRCC tumors might be associated with inactivation of one or more of these genes (36-38).”
Optimal Management of Metastatic Renal Cell Carcinoma: Current Status
Escudier, B. J., Albiges, L. K., & Sonpavde, G. (2013) · Drugs · doi:10.1007/s40265-013-0043-1 · Cited by 98
“TFEB involves a translocation between chromosome 6 and chromosome 11, t [6, 11] (p21;q13), and generally occurs the pediatric population [16].”
BackgroundZheng, Q., Li, P., Zhou, X., Qiang, Y., Fan, J., Lin, Y., Chen, Y., Guo, J., Wang, F., Xue, H., et al. (2021) · Theranostics · doi:10.7150/thno.60233 · Cited by 100
“The systemic sequencing has shown that ccRCC harbors mutations in a number of chromatin modifier genes, including PBRM1, SETD2, BAP1, and KDM5C [11, 12].”
BackgroundTandem duplication of chromosomal segments is common in ovarian and breast cancer genomes
McBride, D. J., Etemadmoghadam, D., Cooke, S. L., Alsop, K., George, J., Butler, A. P., Cho, J., Galappaththige, D., Greenman, C., Howarth, K., et al. (2012) · The Journal of Pathology · doi:10.1002/path.4042 · Cited by 97
Self-citationПили, Р., Liu, G., Chintala, S., Verheul, H. M. W., Rehman, S., Attwood, K. M., Lodge, M. A., Wahl, R. L., Martin, J. I., Miles, K. M., et al. (2017) · British Journal of Cancer · doi:10.1038/bjc.2017.33 · Cited by 97
“As shown also in other solid tumour types, histone modifier genes may have a role in ccRCC tumourigenesis (Dalgliesh et al, 2010).”
BackgroundThe multifaceted von Hippel–Lindau tumour suppressor protein
Robinson, C. M., & Ohh, M. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.02.026 · Cited by 101
“These include a component of the SWI/SNF chromatin remodelling complex PBRM1 (encoding Polybromo 1) [67], the histone methyltransferase SETD2 and the histone demethylases UTX (KDM6A) and JARID1C (KDM5C) [68,69].”
BackgroundEpigenetic modifiers: activities in renal cell carcinoma
de Cubas, A. A., & Rathmell, W. K. (2018) · Nature Reviews Urology · doi:10.1038/s41585-018-0052-7 · Cited by 97
Chowdhury, B., Porter, E. G. P., Stewart, J. C., Ferreira, C. R., Schipma, M. J., & Dykhuizen, E. C. (2016) · PLoS ONE · doi:10.1371/journal.pone.0153718 · Cited by 102
Genomics and epigenomics of renal cell carcinoma
Maher, E. R. (2012) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2012.06.003 · Cited by 93
Two sides to every story: the HIF-dependent and HIF-independent functions of pVHL
Li, M., & Kim, W. Y. (2010) · Journal of Cellular and Molecular Medicine · doi:10.1111/j.1582-4934.2010.01238.x · Cited by 98
“Indeed, whole exosome sequencing from sporadic RCCs detected a significant, but low frequency of truncating mutations in HIF1 suggesting that in RCC it may function as a tumour suppressor [43].”
BackgroundLoss of chromosome Y in primary tumors
Qi, M., Pang, J., Mitsiades, I. R., Lane, A. A., & Rheinbay, E. (2023) · Cell · doi:10.1016/j.cell.2023.06.006 · Cited by 96
Hahn, M. A., Dickson, K.-A., Jackson, S., Clarkson, A., Gill, A. J., & Marsh, D. J. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr490 · Cited by 91
“Although cancer-associated mutations have been reported to affect methylation of core histones (36,37), this is the first report of pathogenic mutations regulating monoubiquitination of a histone.”
BackgroundBaştürk, O., Berger, M. F., Yamaguchi, H., Adsay, V. N., Askan, G., Bhanot, U. K., Zehir, A., Carneiro, F., Hong, S., Zamboni, G., et al. (2017) · Modern Pathology · doi:10.1038/modpathol.2017.60 · Cited by 95
SETting the Stage for Cancer Development: SETD2 and the Consequences of Lost MethylationPreprint
Fahey, C. C., & Davis, I. J. (2017) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a026468 · Cited by 92
Shelar, S. B., Shim, E., Brinkley, G. J., Kundu, A., Carobbio, F., Poston, T. L., Tan, J. C., Parekh, V., Benson, D. G., Crossman, D. K., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1727 · Cited by 89
“demethylase, have been identified in renal cancer (45, 46).”
BackgroundCheng, Z., Cheung, P., Kuo, A. J., Yukl, E. T., Wilmot, C. M., Gozani, O., & Patel, D. J. (2014) · Genes & Development · doi:10.1101/gad.246561.114 · Cited by 91
“The state of methylation at H3K36 is linked to dramatically different oncogenic consequences (Dalgliesh et al. 2010; Kuo et al. 2011; Black et al. 2013).”
BackgroundRNF144A, an E3 ubiquitin ligase for DNA-PKcs, promotes apoptosis during DNA damage
Ho, S.-R., Mahanic, C. S., Lee, Y.-J., & Lin, W.-C. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323107111 · Cited by 88
Rare insights into cancer biology
Adam, J., Yang, M., Soga, T., & Pollard, P. J. (2013) · Oncogene · doi:10.1038/onc.2013.222 · Cited by 90
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3
Prickaerts, P., Adriaens, M. E., van den Beucken, T., Koch, E., Dubois, L. J., Dahlmans, V. E. H., Gits, C. M. M., Evelo, C. T., Chan‐Seng‐Yue, M., Wouters, B. G., et al. (2016) · Epigenetics & Chromatin · doi:10.1186/s13072-016-0086-0 · Cited by 91
Tian, X., Zhang, S., Liu, H., Zhang, Y., Blair, C., Mercola, D., Sassone‐Corsi, P., & Zi, X. (2013) · Current Cancer Drug Targets · doi:10.2174/1568009611313050007 · Cited by 90
“N IH -PA Author M anuscript N IH -PA Author M anuscript N IH -PA Author M anuscript JHDMs Jumonji C domain-containing histone demethylase JmjC Jumonji C KDM demethylases KMT histone lysine methyltransferases LSD1 Lysine-specific demethylase 1 MBD methyl-CpG-binding domain Ndy Not dead yet MAO monoamine oxidase MEFs mo…”
InfluentialInactivation of Merlin in malignant mesothelioma cells and the Hippo signaling cascade dysregulation
Sekido, Y. (2011) · Pathology International · doi:10.1111/j.1440-1827.2011.02666.x · Cited by 90
The genetics of melanoma: recent advances
Hill, V. K., Gartner, J. J., Samuels, Y., & Goldstein, A. M. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153429 · Cited by 86
Grampp, S., Platt, J. L., Lauer, V., Salama, R. A., Kranz, F., Neumann, V. K., Wach, S., Stöhr, C., Hartmann, A., Eckardt, K., et al. (2016) · Nature Communications · doi:10.1038/ncomms13183 · Cited by 88
Epigenetic Deregulation of Apoptosis in Cancers
Ozyerli‐Goknar, E., & Onder, T. B. (2021) · Cancers · doi:10.3390/cancers13133210 · Cited by 94
“SETD2-inactivating mutations are associated with poor outcome and disease relapse in renal cell carcinoma [56] and pediatric acute lymphoblastic leukemia [57].”
BackgroundHacker, K. E., Fahey, C. C., Shinsky, S. A., Chiang, Y.-C., DiFiore, J. V., Jha, D. K., Vo, A. H., Shavit, J. A., Davis, I. J., Strahl, B. D., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.739375 · Cited by 90
“musculus were aligned using ClustalOmega (56) and annotated with reported SETD2 mutations in ccRCC (1, 4, 11, 12).”
BackgroundMethodInfluentialLi, J., Ming, Z., Yang, L., Wang, T., Liu, G., & Ma, Q. (2022) · Genes & Diseases · doi:10.1016/j.gendis.2022.04.007 · Cited by 89
Wilms Tumor Chromatin Profiles Highlight Stem Cell Properties and a Renal Developmental Network
Aiden, A. P., Rivera, M. N., Rheinbay, E., Ku, M., Coffman, E. J., Truong, T. T., Vargas, S. O., Lander, E. S., Haber, D. A., & Bernstein, B. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.016 · Cited by 88
“By contrast, cellular reprogramming may play a more substantial role in adult tumors, which are associated with numerous mutations including alterations in chromatin modifying enzymes (Dalgliesh et al., 2010).”
BackgroundHigh-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma
Ho, T. H., Park, I. Y., Zhao, H., Tong, P., Champion, M. D., Yan, H., Monzon, F. A., Hoang, A. G., Tamboli, P., Parker, A. S., et al. (2015) · Oncogene · doi:10.1038/onc.2015.221 · Cited by 90
“Similar to published genome-wide analyses of patient-derived biopsy tissue (3, 6, 31), ChIP sequencing in whole tissue presents logistical challenges.”
Self-citationRacial difference in histologic subtype of renal cell carcinoma
Olshan, A. F., Kuo, T., Meyer, A., Nielsen, M. E., Purdue, M. P., & Rathmell, W. K. (2013) · Cancer Medicine · doi:10.1002/cam4.110 · Cited by 84
“Notably, clear cell RCC is associated with cytogenetic loss of chromosome 3p, encompassing four of the most commonly mutated genes in this cancer: the closely linked Von Hippel–Lindau (VHL) tumor suppressor gene which has been identified to be inactivated in up to 92% of cases [5], and the more recently recognized hig…”
BackgroundPatient-derived xenografts as in vivo models for research in urological malignancies
Inoue, T., Terada, N., Kobayashi, T., & Ogawa, O. (2017) · Nature Reviews Urology · doi:10.1038/nrurol.2017.19 · Cited by 88
Mutations and epimutations in the origin of cancer
Peltomäki, P. (2011) · Experimental Cell Research · doi:10.1016/j.yexcr.2011.12.001 · Cited by 88
Duns, G., Hofstra, R. M. W., Sietzema, J. G., Hollema, H., van Duivenbode, I., Kuik, A., Giezen, C., Osinga, J., de Boer-Bergsma, J. J., Bijnen, H., et al. (2012) · Human Mutation · doi:10.1002/humu.22090 · Cited by 83
Uzilov, A. V., Ding, W., Fink, M. Y., Antipin, Y., Brohl, A. S., Davis, C., Lau, C. Y., Pandya, C., Shah, H., Kasai, Y., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0313-0 · Cited by 83
“In both of these cases, renal cell carcinoma, a cancer with a relatively high frequency of NF2 mutation [52], was high-ranked on the list of considered diagnoses based on standard pathologic assessment.”
Background
Metadata
- Authors
- Dalgliesh, G. L., Furge, K., Greenman, C., Chen, L., Bignell, G., Butler, A., Davies, H., Edkins, S., Hardy, C., Latimer, C., Teague, J., Andrews, J., Barthorpe, S., Beare, D., Buck, G., Campbell, P. J., Forbes, S., Jia, M., Jones, D., Knott, H., Kok, C. Y., Lau, K. W., Leroy, C., Lin, M.-L., McBride, D. J., Maddison, M., Maguire, S., McLay, K., Menzies, A., Mironenko, T., Mulderrig, L., Mudie, L., O’Meara, S., Pleasance, E., Rajasingham, A., Shepherd, R., Smith, R., Stebbings, L., Stephens, P., Tang, G., Tarpey, P. S., Turrell, K., Dykema, K. J., Khoo, S. K., Petillo, D., Wondergem, B., Anema, J., Kahnoski, R. J., Teh, B. T., Stratton, M. R., & Futreal, P. A.
- Affiliations
- Wellcome Sanger Institute (GB)
- Van Andel Institute (US)
- Spectrum Health (US)
- Institute of Cancer Research (GB)
- Corresponding author
- Teh, Bin Tean
- Stratton, Michael R.
- Futreal, P. Andrew
- ORCID
- Dalgliesh, Gillian L.
- Greenman, Chris
- Chen, Lina
- Davies, Helen
- Edkins, Sarah
- Latimer, Calli
- Teague, Jon
- Barthorpe, Syd
- Buck, Gemma
- Campbell, Peter J.
- Jia, Mingming
- Jones, David
- Lau, King Wai
- Lin, Meng-Lay
- McBride, David J.
- Menzies, Andrew
- Mironenko, Tatiana
- Pleasance, Erin
- Shepherd, Rebecca
- Tarpey, Patrick S.
- Khoo, Sok Kean
- Petillo, David
- Kahnoski, Richard J.
- Teh, Bin Tean
- Stratton, Michael R.
- Futreal, P. Andrew
- Venue
- Nature
- Published
- 2010-01
- Volume
- 463
- Issue
- 7279
- Pages
- 360-363
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2820242
- OpenAlex
- W2079212177
- Cited by
- 1,173
- References
- 28
- Citations by year
- 2026: 20 · 2025: 26 · 2024: 33 · 2023: 43 · 2022: 40 · 2021: 58 · 2020: 63 · 2019: 54 · 2018: 66 · 2017: 65 · 2016: 91 · 2015: 85 · 2014: 119 · 2013: 125 · 2012: 114
- FWCI
- 109.36
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Funders
- Wellcome Trust (077012/Z/05/Z, 082359, 077012, 088340, 093867)
- Topics
- Health Sciences › Medicine › Oncology › Renal cell carcinoma treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- clear cell renal cell carcinoma, somatic mutations, histone-modifying enzymes, SETD2, JARID1C, KDM6A, neurofibromatosis type 2, VHL, chromatin modification, histone H3 lysine 36 methylation, histone H3 lysine 4 demethylation, tumor suppressor, cancer gene identification
- MeSH terms
- Carcinoma, Renal Cell, Chromatin, Histones, Humans, Kidney Neoplasms, Mutation, Nuclear Proteins, Oxidoreductases, N-Demethylating, Histone-Lysine N-Methyltransferase, Cell Hypoxia, Gene Expression Regulation, Neoplastic, Genes, Neurofibromatosis 2, Sequence Analysis, DNA, Histone Demethylases
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
